offtracker 2.10.9__zip → 2.10.11__zip

{offtracker-2.10.9/offtracker.egg-info → offtracker-2.10.11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: offtracker
-Version: 2.10.9
+Version: 2.10.11
 Summary: Tracking-seq data analysis
 Home-page: https://github.com/Lan-lab/offtracker
 Author: Runda Xu
@@ -78,6 +78,9 @@ offtracker_candidates.py -t 8 -g hg38 \
 --name 'VEGFA2' --sgrna 'GACCCCCTCCACCCCGCCTC' --pam 'NGG' \
 -o /Your_Path_To_Candidates_Folder
 
+# if analyzing Cas12a, whose pam is upstream of the sgRNA, add this:
+--pam_location 'upstream'
+
 ```
 
 

{offtracker-2.10.9 → offtracker-2.10.11}/README.md

@@ -66,6 +66,9 @@ offtracker_candidates.py -t 8 -g hg38 \
 --name 'VEGFA2' --sgrna 'GACCCCCTCCACCCCGCCTC' --pam 'NGG' \
 -o /Your_Path_To_Candidates_Folder
 
+# if analyzing Cas12a, whose pam is upstream of the sgRNA, add this:
+--pam_location 'upstream'
+
 ```
 
 

{offtracker-2.10.9 → offtracker-2.10.11}/offtracker/_version.py

@@ -1,4 +1,4 @@
-__version__ = "2.10.9"
+__version__ = "2.10.11"
 # 2023.08.11. v1.1.0	adding a option for not normalizing the bw file
 # 2023.10.26. v1.9.0	prerelease for v2.0
 # 2023.10.27. v2.0.0	大更新，还没微调
@@ -35,4 +35,6 @@ __version__ = "2.10.9"
 # 2025.06.05. v2.10.0	增加了QC模块。保留了负数score的记录，并在plot时显示为红字。增加了 "--ignore_chr" 用于跳过common chr过滤。
 # 2025.06.17. v2.10.7   修复翻新代码结构导致的bug
 # 2025.06.27. v2.10.8   将 chmod 放在了 setup.py 里
-# 2025.06.28. v2.10.9   现在 pip 都是从 wheel 安装，不再运行 setup.py，所以增加一个 offtracker_init.py
+# 2025.06.28. v2.10.9   现在 pip 都是从 wheel 安装，不再运行 setup.py，所以增加一个 offtracker_init.py
+# 2025.06.28. v2.10.10  直接塞 script 里试试
+# 2025.06.28. v2.10.11  回滚到2.10.9外加修正

{offtracker-2.10.9 → offtracker-2.10.11/offtracker.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: offtracker
-Version: 2.10.9
+Version: 2.10.11
 Summary: Tracking-seq data analysis
 Home-page: https://github.com/Lan-lab/offtracker
 Author: Runda Xu
@@ -78,6 +78,9 @@ offtracker_candidates.py -t 8 -g hg38 \
 --name 'VEGFA2' --sgrna 'GACCCCCTCCACCCCGCCTC' --pam 'NGG' \
 -o /Your_Path_To_Candidates_Folder
 
+# if analyzing Cas12a, whose pam is upstream of the sgRNA, add this:
+--pam_location 'upstream'
+
 ```
 
 

{offtracker-2.10.9 → offtracker-2.10.11}/offtracker.egg-info/requires.txt

@@ -1,5 +1,5 @@
 pandas
 numpy
-biopython
+biopython<=1.85
 pybedtools
 pyyaml

offtracker-2.10.11/scripts/offtracker_config.py

@@ -0,0 +1,107 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+# 2023.08.11. adding a option for not normalizing the bw file
+# 2025.05.22. refine the structure
+# 2025.06.05. 增加 ignore_chr 选项，默认只取 common chromosomes，用于 1.1_bed2fr.py
+
+import argparse
+import os, glob, yaml
+import pandas as pd
+import shutil, re
+import offtracker
+import offtracker.X_sequence as xseq
+script_dir = os.path.abspath(os.path.dirname(offtracker.__file__))
+utility_dir = os.path.join(script_dir, 'utility')
+file_path = os.path.join(utility_dir, 'bedGraphToBigWig')
+file_stat = os.stat(file_path)
+file_mode = oct(file_stat.st_mode & 0o777)
+if file_mode != '0o755':
+    try:
+        os.chmod( os.path.join(utility_dir, 'bedGraphToBigWig'), 0o755)
+    except:
+        print('offtracker may be installed in root but not initialized. Please run "offtracker_init.py" with root permission first.')
+
+###
+def main():
+    parser = argparse.ArgumentParser()
+    parser.description='Mapping fastq files of Tracking-seq.'
+    parser.add_argument('-f','--folder', type=str, required=True,  help='Directory of the input folder' )
+    parser.add_argument('-r','--ref'   , type=str, required=True,  help='The fasta file of reference genome')
+    parser.add_argument('-i','--index' , type=str, required=True,  help='The index file of chromap')
+    parser.add_argument('-g','--genome', type=str, required=True,  help='File of chromosome sizes, or "hg38", "mm10" ')
+    parser.add_argument('-o','--outdir', type=str, default='same', help='The output folder')
+    parser.add_argument('--subfolder'  , type=int, default=0,      help='subfolder level')
+    parser.add_argument('-t','--thread', type=int, default=4,      help='Number of threads to be used')
+    parser.add_argument('--blacklist'  , type=str, default='same', help='Blacklist of genome regions in bed format. "none" for no filter')
+    parser.add_argument('--binsize'    , type=str, default=100,    help='Bin size for calculating bw residue')
+    parser.add_argument('--normalize'  , type=str, default='True', help='Whether to normalize the BigWig file. "True" or "False"')
+    parser.add_argument('--ignore_chr' , action='store_true', help='If not set, only chr1-chr22, chrX, chrY, chrM will be analyzed.')
+
+
+    args = parser.parse_args()
+
+    if (args.genome == 'hg38') or (args.genome == 'mm10'):
+        dir_chrom_sizes = os.path.join(utility_dir, f'{args.genome}.chrom.sizes')
+    else:
+        dir_chrom_sizes = args.genome
+
+    if (args.normalize != 'True') & (args.normalize != 'False'):
+        raise ValueError('Please provide "True" or "False" for "--normalize"')
+
+    if args.blacklist == 'same':
+        assert ((args.genome == 'hg38') or (args.genome == 'mm10')), 'Please provide blacklist file, or "--blacklist none" to skip'
+        args.blacklist = args.genome
+        
+    if (args.blacklist == 'hg38') or (args.blacklist == 'mm10'):
+        blacklist = os.path.join(utility_dir, f'offtracker_blacklist_{args.blacklist}.merged.bed')
+    else:
+        blacklist = args.blacklist
+
+    if args.outdir == 'same':
+        args.outdir = args.folder
+    else:
+        if not os.path.exists(args.outdir):
+            os.makedirs(args.outdir)
+
+    if args.ignore_chr:
+        args.ignore_chr = '--ignore_chr'
+    else:
+        args.ignore_chr = ''
+
+    # 搜索 folder 的 n级子目录下的所有 fastq/fastq.gz/fq/fq.gz 文件
+    sample_names, files_R1, files_R2 = xseq.detect_fastq(args.folder, n_subfolder=args.subfolder)
+
+    assert not isinstance(sample_names, str), 'No fastq file is detected!'
+
+    dict_yaml = {
+        # fastq 信息
+        'files_R1':dict(zip(sample_names,files_R1)),
+        'files_R2':dict(zip(sample_names,files_R2)), # 单端 files_R2=[] 结果会自动为 {}
+        # 输入输出文件夹
+        'input_dir':args.folder,
+        'output_dir':args.outdir,
+        # 运行参数
+        'thread':args.thread,
+        'index':args.index,
+        'fasta':args.ref,
+        'binsize':args.binsize,
+        'blacklist':blacklist,
+        'genomelen':dir_chrom_sizes,
+        'normalize':args.normalize,
+        'utility_dir':utility_dir,
+        'ignore_chr':args.ignore_chr,
+        }
+
+    with open( os.path.join(args.outdir,'config.yaml'), 'w') as outfile:
+        yaml.dump(dict_yaml, outfile, default_flow_style=False)
+
+    snakefile = os.path.join(script_dir, 'snakefile/Snakefile_offtracker.smk')
+    shutil.copy(snakefile, os.path.join(args.outdir,'Snakefile'))
+
+    return 'config_main finished'
+
+if __name__ == '__main__' :
+    result = main()
+    print(result)
+

offtracker-2.10.11/scripts/offtracker_qc.py

@@ -0,0 +1,73 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+THIS_VERSION = '0.4.1'
+
+import argparse
+import os, glob, yaml
+import pandas as pd
+import shutil, re
+import offtracker
+import offtracker.X_sequence as xseq
+
+script_dir = os.path.abspath(os.path.dirname(offtracker.__file__))
+utility_dir = os.path.join(script_dir, 'utility')
+file_path = os.path.join(utility_dir, 'bedGraphToBigWig')
+file_stat = os.stat(file_path)
+file_mode = oct(file_stat.st_mode & 0o777)
+if file_mode != '0o755':
+    try:
+        os.chmod( os.path.join(utility_dir, 'bedGraphToBigWig'), 0o755)
+    except:
+        print('offtracker may be installed in root but not initialized. Please run "offtracker_init.py" with root permission first.')
+
+###
+def main():
+    parser = argparse.ArgumentParser()
+    parser.description=f'xbulk_qc v{THIS_VERSION}. QC and trim fastq files.'
+    parser.add_argument('-f','--folder', type=str, required=True,        help='Directory of the input folder' )
+    parser.add_argument('-o','--outdir', type=str, default='same',       help='The output folder')
+    parser.add_argument('--subfolder'  , type=int, default=0,            help='subfolder level')
+    parser.add_argument('-t','--thread', type=int, default=8,            help='Number of threads to be used')
+
+    args = parser.parse_args()
+
+    # 自动化的参数调整和报错
+    if args.outdir == 'same':
+        args.outdir = os.path.join(args.folder,'Trimmed_data')
+        if not os.path.exists( args.outdir ):
+            os.makedirs( args.outdir )
+    else:
+        if not os.path.exists(args.outdir):
+            os.makedirs(args.outdir)
+
+    # 搜索 folder 的 n级子目录下的所有 fastq/fastq.gz/fq/fq.gz 文件
+    sample_names, files_R1, files_R2 = xseq.detect_fastq(args.folder, n_subfolder=args.subfolder)
+
+    assert not isinstance(sample_names, str), 'No fastq file is detected!'
+
+    dict_yaml = {
+        # fastq 信息
+        'files_R1':dict(zip(sample_names,files_R1)),
+        'files_R2':dict(zip(sample_names,files_R2)), # 单端 files_R2=[] 结果会自动为 {}
+        # 输入输出文件夹
+        'input_dir':args.folder,
+        'output_dir':args.outdir,
+        # 运行参数
+        'thread':args.thread,
+        'utility_dir':utility_dir
+        }
+
+
+    with open( os.path.join(args.outdir,'config.yaml'), 'w', encoding='utf-8') as outfile:
+        yaml.dump(dict_yaml, outfile, default_flow_style=False)
+
+    snakefile = os.path.join(script_dir, 'snakefile/Snakefile_QC.smk')
+    shutil.copy(snakefile, os.path.join(args.outdir,'Snakefile'))
+
+    return 'config_qc finished'
+
+if __name__ == '__main__' :
+    result = main()
+    print(result)
+

{offtracker-2.10.9 → offtracker-2.10.11}/setup.py

@@ -6,10 +6,6 @@ import io, os
 # from shutil import rmtree
 from setuptools import setup
 
-# import pkg_resources
-from importlib_metadata import distribution
-from setuptools.command.install import install
-from setuptools.command.develop import develop
 
 #
 NAME = 'offtracker'
@@ -30,7 +26,7 @@ with open(os.path.join(here, package_folder, '_version.py'),'r',encoding='utf-8'
 
 # requirements
 REQUIRED = [
-   'pandas', 'numpy', 'biopython', 'pybedtools', 'pyyaml', 
+   'pandas', 'numpy', 'biopython<=1.85', 'pybedtools', 'pyyaml', 
 ]
 ## pybedtools may be not supported in Windows
 
@@ -41,24 +37,6 @@ except FileNotFoundError:
     long_description = DESCRIPTION
 
 
-class PostInstallCommand(install):
-    def run(self):
-        install.run(self)
-        # 获取文件位置
-        dist = distribution('offtracker')
-        package_path = dist.locate_file('')
-        utility_dir = os.path.join(package_path, 'offtracker/utility')
-        os.chmod( os.path.join(utility_dir, 'bedGraphToBigWig'), 0o755)
-
-class PostDevelopCommand(develop):
-    def run(self):
-        develop.run(self)
-        # 获取文件位置
-        dist = distribution('offtracker')
-        package_path = dist.locate_file('')
-        utility_dir = os.path.join(package_path, 'offtracker/utility')
-        os.chmod( os.path.join(utility_dir, 'bedGraphToBigWig'), 0o755)
-
 setup(
     name=NAME,
     version=VERSION,
@@ -71,16 +49,12 @@ setup(
     python_requires=REQUIRES_PYTHON,
     packages=['offtracker'],
     package_data={'offtracker': ['snakefile/*','utility/*']},
-    cmdclass={
-        'install': PostInstallCommand,
-        'develop': PostDevelopCommand,
-    },
-    scripts = ['scripts/offtracker_init.py',
-               'scripts/offtracker_qc.py',
-               'scripts/offtracker_config.py',
-               'scripts/offtracker_candidates.py',
-               'scripts/offtracker_analysis.py',
-               'scripts/offtracker_plot.py'],
+    scripts = [ 'scripts/offtracker_init.py',
+                'scripts/offtracker_qc.py',
+                'scripts/offtracker_config.py',
+                'scripts/offtracker_candidates.py',
+                'scripts/offtracker_analysis.py',
+                'scripts/offtracker_plot.py'],
     install_requires=REQUIRED,
     include_package_data=True
 )

offtracker-2.10.9/scripts/offtracker_config.py

@@ -1,97 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-# 2023.08.11. adding a option for not normalizing the bw file
-# 2025.05.22. refine the structure
-# 2025.06.05. 增加 ignore_chr 选项，默认只取 common chromosomes，用于 1.1_bed2fr.py
-
-import argparse
-import os, glob, yaml
-import pandas as pd
-import shutil, re
-import offtracker
-import offtracker.X_sequence as xseq
-script_dir = os.path.abspath(os.path.dirname(offtracker.__file__))
-utility_dir = os.path.join(script_dir, 'utility')
-try:
-    os.chmod( os.path.join(utility_dir, 'bedGraphToBigWig'), 0o755)
-except:
-    print('offtracker may be installed in root but not initialized. Please run "offtracker_init.py" with root permission first.')
-
-###
-parser = argparse.ArgumentParser()
-parser.description='Mapping fastq files of Tracking-seq.'
-parser.add_argument('-f','--folder', type=str, required=True,  help='Directory of the input folder' )
-parser.add_argument('-r','--ref'   , type=str, required=True,  help='The fasta file of reference genome')
-parser.add_argument('-i','--index' , type=str, required=True,  help='The index file of chromap')
-parser.add_argument('-g','--genome', type=str, required=True,  help='File of chromosome sizes, or "hg38", "mm10" ')
-parser.add_argument('-o','--outdir', type=str, default='same', help='The output folder')
-parser.add_argument('--subfolder'  , type=int, default=0,      help='subfolder level')
-parser.add_argument('-t','--thread', type=int, default=4,      help='Number of threads to be used')
-parser.add_argument('--blacklist'  , type=str, default='same', help='Blacklist of genome regions in bed format. "none" for no filter')
-parser.add_argument('--binsize'    , type=str, default=100,    help='Bin size for calculating bw residue')
-parser.add_argument('--normalize'  , type=str, default='True', help='Whether to normalize the BigWig file. "True" or "False"')
-parser.add_argument('--ignore_chr' , action='store_true', help='If not set, only chr1-chr22, chrX, chrY, chrM will be analyzed.')
-
-
-args = parser.parse_args()
-
-if (args.genome == 'hg38') or (args.genome == 'mm10'):
-    dir_chrom_sizes = os.path.join(utility_dir, f'{args.genome}.chrom.sizes')
-else:
-    dir_chrom_sizes = args.genome
-
-if (args.normalize != 'True') & (args.normalize != 'False'):
-    raise ValueError('Please provide "True" or "False" for "--normalize"')
-
-if args.blacklist == 'same':
-    assert ((args.genome == 'hg38') or (args.genome == 'mm10')), 'Please provide blacklist file, or "--blacklist none" to skip'
-    args.blacklist = args.genome
-    
-if (args.blacklist == 'hg38') or (args.blacklist == 'mm10'):
-    blacklist = os.path.join(utility_dir, f'offtracker_blacklist_{args.blacklist}.merged.bed')
-else:
-    blacklist = args.blacklist
-
-if args.outdir == 'same':
-    args.outdir = args.folder
-else:
-    if not os.path.exists(args.outdir):
-        os.makedirs(args.outdir)
-
-if args.ignore_chr:
-    args.ignore_chr = '--ignore_chr'
-else:
-    args.ignore_chr = ''
-
-# 搜索 folder 的 n级子目录下的所有 fastq/fastq.gz/fq/fq.gz 文件
-sample_names, files_R1, files_R2 = xseq.detect_fastq(args.folder, n_subfolder=args.subfolder)
-
-assert not isinstance(sample_names, str), 'No fastq file is detected!'
-
-dict_yaml = {
-    # fastq 信息
-    'files_R1':dict(zip(sample_names,files_R1)),
-    'files_R2':dict(zip(sample_names,files_R2)), # 单端 files_R2=[] 结果会自动为 {}
-    # 输入输出文件夹
-    'input_dir':args.folder,
-    'output_dir':args.outdir,
-    # 运行参数
-    'thread':args.thread,
-    'index':args.index,
-    'fasta':args.ref,
-    'binsize':args.binsize,
-    'blacklist':blacklist,
-    'genomelen':dir_chrom_sizes,
-    'normalize':args.normalize,
-    'utility_dir':utility_dir,
-    'ignore_chr':args.ignore_chr,
-    }
-
-with open( os.path.join(args.outdir,'config.yaml'), 'w') as outfile:
-    yaml.dump(dict_yaml, outfile, default_flow_style=False)
-
-snakefile = os.path.join(script_dir, 'snakefile/Snakefile_offtracker.smk')
-shutil.copy(snakefile, os.path.join(args.outdir,'Snakefile'))
-
-

offtracker-2.10.9/scripts/offtracker_qc.py

@@ -1,63 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-THIS_VERSION = '0.4.1'
-
-import argparse
-import os, glob, yaml
-import pandas as pd
-import shutil, re
-import offtracker
-import offtracker.X_sequence as xseq
-
-script_dir = os.path.abspath(os.path.dirname(offtracker.__file__))
-utility_dir = os.path.join(script_dir, 'utility')
-try:
-    os.chmod( os.path.join(utility_dir, 'bedGraphToBigWig'), 0o755)
-except:
-    print('offtracker may be installed in root but not initialized. Please run "offtracker_init.py" with root permission first.')
-
-###
-parser = argparse.ArgumentParser()
-parser.description=f'xbulk_qc v{THIS_VERSION}. QC and trim fastq files.'
-parser.add_argument('-f','--folder', type=str, required=True,        help='Directory of the input folder' )
-parser.add_argument('-o','--outdir', type=str, default='same',       help='The output folder')
-parser.add_argument('--subfolder'  , type=int, default=0,            help='subfolder level')
-parser.add_argument('-t','--thread', type=int, default=8,            help='Number of threads to be used')
-
-args = parser.parse_args()
-
-# 自动化的参数调整和报错
-if args.outdir == 'same':
-    args.outdir = os.path.join(args.folder,'Trimmed_data')
-    if not os.path.exists( args.outdir ):
-        os.makedirs( args.outdir )
-else:
-    if not os.path.exists(args.outdir):
-        os.makedirs(args.outdir)
-
-# 搜索 folder 的 n级子目录下的所有 fastq/fastq.gz/fq/fq.gz 文件
-sample_names, files_R1, files_R2 = xseq.detect_fastq(args.folder, n_subfolder=args.subfolder)
-
-assert not isinstance(sample_names, str), 'No fastq file is detected!'
-
-dict_yaml = {
-    # fastq 信息
-    'files_R1':dict(zip(sample_names,files_R1)),
-    'files_R2':dict(zip(sample_names,files_R2)), # 单端 files_R2=[] 结果会自动为 {}
-    # 输入输出文件夹
-    'input_dir':args.folder,
-    'output_dir':args.outdir,
-    # 运行参数
-    'thread':args.thread,
-    'utility_dir':utility_dir
-    }
-
-
-with open( os.path.join(args.outdir,'config.yaml'), 'w', encoding='utf-8') as outfile:
-    yaml.dump(dict_yaml, outfile, default_flow_style=False)
-
-snakefile = os.path.join(script_dir, 'snakefile/Snakefile_QC.smk')
-shutil.copy(snakefile, os.path.join(args.outdir,'Snakefile'))
-
-